00_Add_to_Reference.readme

This provides instructions for adding extra sequences to a reference genome 
prior to mapping your reads. Reasons for doing this would be:
	1) if your celline contains inserted genetic contructs, 
		e.g. for CRISPR, or for fluorescently labelling your cells. 
	2) if you've added spike-in transcripts to your sample.

1) This will require manually creating the GTF annotations for your 
	particular construct. If you have a GenBank file (.gbk) you can use:
	0_GBK2FASTA.pl
	to extract the raw sequence of the construct to append to the genome.

2) If using the ERCC spike in, you must download the sequences from the 
	manufacturer, i.e. the "ERCC Controls Annotation" file from: 
	https://www.thermofisher.com/order/catalog/product/4456740
	then run:
	0_Make_ERCC_fasta_and_gtf.pl ERCC_Controls_Annotation.txt
	this will create a fasta and gtf file for the ERCCs in your working 
	directory which you can append to the reference genome.

Append your extra gtf and fasta files to the existing reference fasta and gtf using "cat" :
cat ERCC_Controls.fa >> ref.fa
cat ERCC_Controls.gtf >> ref.gtf